The demand for natural compounds to replace synthetic additives has aroused the interest of different sectors of society, especially the scientific community, due to their safety, biocompatibility, biodegradability and low toxicity. Alternative sources for antimicrobial compounds have been explored, such as fruit pomace. These by-products have essential compounds in their composition with different potential for application in food and packaging. In this context, this review systematizes the use of pomace from different fruits as a source of antibacterial compounds. Also, it summarizes the extraction methods and the applications of these compounds. Grape pomace, cranberry, and apple extracts are the most explored for antibacterial control, especially against genus Listeria, Salmonella, Staphylococcus, and Escherichia. In addition, phenolic acids, anthocyanins, flavonoids, and proanthocyanins are the main compounds identified in the studied fruit pomace extracts. In the reviewed articles, the biocompounds recovery is performed by methods with the absence of high temperatures (>80 °C); in some studies, the solid-liquid extraction method at mild temperatures (<30 °C) was well explored, using ethanol and water as solvent. The use of fruit processing by-products for bacterial control highlights the possibility of favoring the three pillars of sustainability (social, economic, and environmental) in the food industry.